docs: custom-experiments guide, earthy brand theme + SEO, planning refresh - #10
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polyfill.io was sold and served malware (2024 supply-chain attack) and is unnecessary for modern browsers. Switch MathJax CDN to unpkg and add a local mathjax.js configuring arithmatex output + re-typeset on navigation.
Colour scheme (defined in HSL): - Default header (Home/About) now dark moss-green instead of indigo blue. - Diátaxis quadrant headers retuned to muted, earthy, brand-adjacent tones: Tutorials sage-green, How-to warm ochre, Reference slate, Explanation teal. All pass WCAG AA (>=4.5:1) with white header text. - Brand amber #CF8A2A is the global link/hover accent in both light and dark schemes (light uses a deeper amber for AA link contrast); brand purple #672E6B added as a secondary accent (header keyline, ==mark==, active ToC). - Dark mode no longer falls back to Material's blue: primary/accent set to 'custom' and re-pointed to the brand palette for the slate scheme. SEO: - site_name set to 'DynVision' (was empty) so <title>/og:site_name populate; redundant header wordmark hidden via CSS (logo already carries it). - Expanded site_description; added Open Graph + Twitter Card meta, keywords, theme-color, and canonical URL in overrides/main.html.
- Add user-guide/custom-experiments.md: how to define an experiment in config_experiments.yaml and run it via the *_model_variations rules (grounded in the real config schema + snake_experiments.smk). Promoted from the 'planned guides' list and wired into the How-to nav. - Replace the completed todo-roadmap.md changelog with a forward-looking todo-development.md tracking planned toolbox improvements (Python 3.12/13, config-driven transforms, provenance logging, config-snapshot isolation, memory-efficient plotting, broader tests, naming cleanup), derived from the design notes in development/planning/. - Trim todo-docs.md down to the live doc gaps (drop resolved changelog). - Remove todo-release-0.1.md (release shipped) and todo-roadmap.md (complete). - Update development/index.md links/counts to point at todo-development.md. Clean mkdocs build from repo root; no link warnings.
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Pull request overview
Documentation-only update that expands the user guide with a new “Custom Experiments” walkthrough, refreshes the MkDocs Material visual theme to an earthy brand palette, improves SEO/social metadata, and updates/reshapes planning docs under docs/development/.
Changes:
- Added a new user guide page explaining how to define/run experiment configs and category sweeps via Snakemake.
- Updated docs theming (HSL-based palette, quadrant headers, brand accents) and added SEO/OpenGraph/Twitter metadata.
- Switched MathJax setup to a local config + CDN script and refreshed planning/roadmap documentation structure.
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/user-guide/index.md | Adds the new Custom Experiments guide to the user-guide index. |
| docs/user-guide/custom-experiments.md | New guide describing experiment/category configuration and Snakemake usage. |
| docs/stylesheets/diataxis.css | Implements the earthy palette, global accents, quadrant header theming, and header wordmark handling. |
| docs/overrides/main.html | Adds canonical/keywords/theme-color + Open Graph/Twitter card metadata. |
| docs/mkdocs.yml | Sets site_name, updates theme palette to custom, adds MathJax JS config, and rewires planning nav. |
| docs/javascripts/mathjax.js | Adds a self-hosted MathJax configuration and re-typeset hook for navigation. |
| docs/development/planning/todo-roadmap.md | Removes the completed roadmap/changelog planning doc. |
| docs/development/planning/todo-release-0.1.md | Removes the release-prep roadmap doc. |
| docs/development/planning/todo-docs.md | Trims to a smaller set of current doc gaps and updates contributor notes. |
| docs/development/planning/todo-development.md | Adds a new toolbox-focused development roadmap document. |
| docs/development/index.md | Updates links and descriptions to match the new planning doc structure. |
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| !!! tip "Timestep budget" | ||
| For most presentation loaders the timeline is `intro + stim + idle` and | ||
| should match `dsteps`. Keep them consistent so the stimulus window falls | ||
| where you expect within the recorded response. |
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idle is used for the initial unrecorded simulation time with null input before dsteps/tsteps start counting
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| snakemake test_model_variations --config category=rctype experiment=flash \ | ||
| --allowed-rules test_model process_test_data |
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| - ⬜ **Custom experiments** — how to define a new entry in | ||
| `config_experiments.yaml` and run it via the `*_model_variations` rules. | ||
| *(added 2026-07-03: [Custom Experiments guide](../../user-guide/custom-experiments.md))* |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Summary
Documentation-only changes across three areas (3 commits,
docs/only — no library/runtime code touched).1. New guide — Custom Experiments (
user-guide/custom-experiments.md)config_experiments.yaml(parameter/data_loader/data_args/ optionalstatus) and run it via thetrain/test/plot_model_variationsrules.snake_experiments.smk; verified the referencedStimulus*DataLoaderclasses exist.2. Earthy brand theme + SEO
primary/accent: custom).site_nameset, expanded description, Open Graph + Twitter Card + keywords + theme-color + canonical URL inoverrides/main.html; redundant header wordmark hidden (logo carries it).3. MathJax self-hosting + polyfill removal
polyfill.ioreference; self-hosted MathJax config (docs/javascripts/mathjax.js) with the CDN as the only external JS dependency.Planning docs refresh
todo-roadmap.md(changelog) and shippedtodo-release-0.1.md.todo-development.md— forward-looking roadmap of planned toolbox improvements (Python 3.12/3.13, config-driven transforms, provenance logging, config-snapshot isolation, memory-efficient plotting, broader tests, naming cleanup).todo-docs.mdto the live doc gaps; updateddevelopment/index.mdlinks/counts.Verification
mkdocs build -f docs/mkdocs.ymlfrom repo root — no link warnings.Note
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workflowscope, since a push tomaintriggers the docs deploy workflow. If the CLI merge is blocked, merge via the web UI.